| Title: | A Tidy Format Datasets of Dengue by Country |
|---|---|
| Description: | Provides a weekly, monthly, yearly summary of dengue cases by state/ province/ country. |
| Authors: | Thiyanga S. Talagala [aut, cre]
|
| Maintainer: | Thiyanga S. Talagala <[email protected]> |
| License: | GPL-3 |
| Version: | 2.1.2 |
| Built: | 2024-10-19 12:22:26 UTC |
| Source: | https://github.com/thiyangt/denguedatahub |
Region/Country-wise dengue and severe dengue cases and deaths since 1980 (Last accessed from the source on 30 January 2023).
americas_annual_dataamericas_annual_data
A tibble with 899134 rows and 5 variables:
Name of the affected region
Name of the country
An indicator for the type of cases (deaths, cases)
cases
year
head(americas_annual_data)head(americas_annual_data)
All dengue cases by week in US states and territories, 2010 - 2023 published by the US Centers for Disease Control and Prevention (CDC)
cdc_casesby_weekcdc_casesby_week
A tibble with 742 rows and 4 variables:
Year
Travel status
Week
Number of reported dengue cases
Accessed from https://www.cdc.gov/dengue/data-research/facts-stats/historic-data.html. Last accessed (Sep 3, 2024)
head(cdc_casesby_week)head(cdc_casesby_week)
Annual dengue cases by age group and sex in US states and territories, 2010 - 2023 published by the US Centers for Disease Control and Prevention (CDC)
cdc_dengue_agesexcdc_dengue_agesex
A tibble with 3900 rows and 7 variables:
Year
Travel status
Age group
Number of male dengue cases
Number of female dengue cases
Accessed from https://www.cdc.gov/dengue/data-research/facts-stats/historic-data.html. Last accessed (Sep 3, 2024)
head(cdc_dengue_agesex)head(cdc_dengue_agesex)
All dengue cases by jurisdiction of residence in US states and territories, 2010 - 2023 published by the US Centers for Disease Control and Prevention (CDC)
cdc_dengue_casesbyjurisdictioncdc_dengue_casesbyjurisdiction
A tibble with 742 rows and 4 variables:
Year
Travel status
Jurisdiction
Dengue counts
Categorization of counts for easy plotting
Additional notes regarding the observation record
Accessed from https://www.cdc.gov/dengue/data-research/facts-stats/historic-data.html. Last accessed (Sep 3, 2024)
head(cdc_dengue_casesbyjurisdiction)head(cdc_dengue_casesbyjurisdiction)
Annual dengue cases by county of residence in US states and territories, 2010 - 2023 published by the US Centers for Disease Control and Prevention (CDC)
cdc_dengue_countyyearcdc_dengue_countyyear
A tibble with 3900 rows and 7 variables:
Reporting Area
Year
Travel status
County
Categorisation of counts for easy visualisations
Additional note about the area
Accessed from https://www.cdc.gov/dengue/data-research/facts-stats/historic-data.html. Last accessed (Sep 3, 2024)
head(cdc_usa_dengue_infection)head(cdc_usa_dengue_infection)
Locally acquired dengue cases by year in the US, 2010 - 2023 published by the US Centers for Disease Control and Prevention (CDC)
cdc_local_dengue_casescdc_local_dengue_cases
A tibble with 14 rows and 3 variables:
Year
Travel status
Number of reported cases
Accessed from https://www.cdc.gov/dengue/data-research/facts-stats/historic-data.html. Last accessed (Sep 3, 2024)
head(cdc_local_dengue_cases)head(cdc_local_dengue_cases)
Travel associated dengue cases by year, 2010 - 2023 in the US, 2010 - 2023 published by the US Centers for Disease Control and Prevention (CDC)
cdc_travel_associated_dengue_casescdc_travel_associated_dengue_cases
A tibble with 14 rows and 3 variables:
Year
Travel status
Number of reported cases
Accessed from https://www.cdc.gov/dengue/data-research/facts-stats/historic-data.html. Last accessed (Sep 3, 2024)
head(cdc_travel_associated_dengue_cases)head(cdc_travel_associated_dengue_cases)
Annual cases of dengue in different areas of the USA
cdc_usa_dengue_infectioncdc_usa_dengue_infection
A tibble with 9170 rows and 38 variables:
Reporting Area
Year
Week
Dengue cases in the current week
Dengue like illness cases in the current week
Severe dengue cases in the current week
https://data.cdc.gov/browse.php?federation_filter=85&format=php&sortBy=alpha&tags=dengue
head(cdc_usa_dengue_infection)head(cdc_usa_dengue_infection)
Annual indigenous and imported dengue cases in mainland China, 2005-2020
china_annual_datachina_annual_data
A tibble with 16 rows and 5 variables:
Year
Number of indigenous dengue cases
Number of imported dengue cases
Number of counties with dengue fever - indigenous cases
Number of counties with dengue fever - imported cases
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8997546/table/ijerph-19-03910-t001/?report=objectonly
head(china_annual_data)head(china_annual_data)
Read weekly epidemiological reports and convert dengue data into tidy format
convert_slwer_to_tidy( year, reports.url, start.date.first, end.date.first, start.date.last, end.date.last, week.no )convert_slwer_to_tidy( year, reports.url, start.date.first, end.date.first, start.date.last, end.date.last, week.no )
year |
year |
reports.url |
URL address vector obtained from get_pdflinks_srilanka |
start.date.first |
starting date of the first report week (format "2006-12-23") |
end.date.first |
endinging date of the first report week (format "2006-12-23") |
start.date.last |
starting date of the last report week (format "2006-12-23") |
end.date.last |
endinging date of the first report week (format "2006-12-23") |
week.no |
report number vector |
Read weekly epidemiological reports and convert dengue data into tidy format
convert_srilanka_wer_to_tidy( year, url.part1 = "https://www.epid.gov.lk", url.part2, start.date.first, end.date.first, start.date.last, end.date.last, week.no )convert_srilanka_wer_to_tidy( year, url.part1 = "https://www.epid.gov.lk", url.part2, start.date.first, end.date.first, start.date.last, end.date.last, week.no )
year |
year |
url.part1 |
first part of the URL, by default "https://www.epid.gov.lk" |
url.part2 |
URL address vector obtained from filter_year_wer_link |
start.date.first |
starting date of the first report week (format "2006-12-23") |
end.date.first |
endinging date of the first report week (format "2006-12-23") |
start.date.last |
starting date of the last report week (format "2006-12-23") |
end.date.last |
endinging date of the first report week (format "2006-12-23") |
week.no |
report number vector |
Download and save weekly epidemiological reports from Epidemiology Unit, Ministry of Health, Sri Lanka (url https://www.epid.gov.lk/weekly-epidemiological-report/weekly-epidemiological-report)
download_pdfwer_srilanka( url = "https://www.epid.gov.lk/weekly-epidemiological-report/weekly-epidemiological-report", folder.name, volume.number )download_pdfwer_srilanka( url = "https://www.epid.gov.lk/weekly-epidemiological-report/weekly-epidemiological-report", folder.name, volume.number )
url |
url of the webpage that you intend to download files. The default is URL of the weekly epidemiological reports page |
folder.name |
create a folder with this name and save the pdf file inside this folder |
volume.number |
Volume number of the epidemiological reports (Volumes corresponds to year) |
Pdf files corresponds to the volume number you specified inside the folder.name
Thiyanga S Talagala
Filter links corresponds to a specific year using the function output get_address
filter_year_wer(year, address)filter_year_wer(year, address)
year |
year that you want to extract the reports |
address |
list or the outout from get_addess function |
Thiyanga S Talagala
Extract links of all downloadable files on a webpage
get_addresses(url)get_addresses(url)
url |
url of the webpage that you intend to download files. |
web addresses of all downloadable files
Thiyanga S Talagala
Get URLs of weekly epidemiological reports from Epidemiology Unit, Ministry of Health, Sri Lanka (url https://www.epid.gov.lk/weekly-epidemiological-report/weekly-epidemiological-report)
get_pdflinks_srilanka( url = "https://www.epid.gov.lk/weekly-epidemiological-report/weekly-epidemiological-report", volume.number )get_pdflinks_srilanka( url = "https://www.epid.gov.lk/weekly-epidemiological-report/weekly-epidemiological-report", volume.number )
url |
url of the webpage that you intend to download files. The default is URL of the weekly epidemiological reports page |
volume.number |
Volume number of the epidemiological reports (Volumes corresponds to year) |
URLS of PDF files corresponds to the volume number
Thiyanga S Talagala
State/Union Territory(UT)-wise dengue/DHF annual deaths and cases since 2017 (Last accessed from the source on 30 January 2023).
india_annual_dataindia_annual_data
A tibble with 432 rows and 5 variables:
Name of the affected states/UTs
An indicator for the type of cases (deaths, cases)
Year
Additional information regarding collected year period
Cases
National Center for Vector Borne Disease Control, Directorate General of Health Services, Ministry of Health and Family Welfare, Government of India.
head(india_annual_data)head(india_annual_data)
Data for imported dengue cases were collected from Korea Centers for Disease Control and Prevention (KCDC)
korea_denguekorea_dengue
A tibble with 33 rows and 7 variables:
Country
Region
Year 2011
Year 2012
Year 2013
Year 2014
Year 2015
Je, Sungmo, Wonjun Bae, Jiyeon Kim, Seung Hyeok Seok, and Eung-Soo Hwang. "Epidemiological characteristics and risk factors of dengue infection in Korean travelers." Journal of Korean Medical Science 31, no. 12 (2016): 1863-1873.
head(korea_dengue)head(korea_dengue)
Country-wise dengue risk levels (Last accessed from the source on 18 January 2023).
level_of_risklevel_of_risk
A tibble with 293 rows and 4 variables:
factor Name of the country
factor Dengue risk level. There are three categories: Frequent or continuous, Sporadic or uncertain, Varies by region. Frequent/continuous risk: evidence of more than 10 dengue cases in at least 3 of the previous 10 years. Sporadic/uncertain risk: evidence of at least 1 locally acquired dengue case during the last 10 years.
factor Region
information last accessed date
The 2024 data accessed from https://www.cdc.gov/dengue/areas-with-risk/index.html.
head(level_of_risk)head(level_of_risk)
Apply min-max transformation
min_max(data, variable.to.minmax, local = FALSE, group.var)min_max(data, variable.to.minmax, local = FALSE, group.var)
data |
tibble that contains cases, groups |
variable.to.minmax |
the variable that we want to tranform using the min-max transformation |
local |
TRUE if you need to apply local minmax transformation |
group.var |
variables that you need to create group-wise |
tibble with minmax transformed applied
Daily cases of dengue in Philippines
philippines_daily_dataphilippines_daily_data
A tibble with 32701 rows and 5 variables:
location
affected and infected number of cases
affected and killed number of cases
date of the week
region name
https://data.humdata.org/dataset/philippine-dengue-cases-and-deaths?
head(philippines_daily_data)head(philippines_daily_data)
Weekly cases of dengue in Sri Lanka
singapore_weekly_datasingapore_weekly_data
A tibble with 18772 rows and 6 variables:
year
week number
Number of dengue cases
head(singapore_weekly_data)head(singapore_weekly_data)
Annual reported dengue cases in Sri Lanka 1989-2021
sl_annualsl_annual
A tibble with 35 rows and 3 variables:
Year
Number of dengue cases
Epidemic: 1 if the year is classified as an epidemic year, 0 otherwise
Source 1: World Health Organization. Dengue Fact Sheet and Situation Report, Sri Lanka. 22 July 2022. Available at: https://cdn.who.int/media/docs/default-source/sri-lanka-documents/dengue-fact-sheet_7-2022-srl.pdf?sfvrsn=49021bd_1. (Accessed: 4 September 2024), Source 2: Weekly Dengue Updates, National Dengue Control Unit, Ministry of Health
head(sl_annual)head(sl_annual)
History of dengue dengue serotypes circulating in Sri Lanka.
sl_dengue_serotypesl_dengue_serotype
A tibble with 35 rows and 3 variables:
Year
Number of dengue cases
Ali, Shahid, Abdul Waheed Khan, Andrew W. Taylor-Robinson, Muhammad Adnan, Shahana Malik, and Saba Gul. "The unprecedented magnitude of the 2017 dengue outbreak in Sri Lanka provides lessons for future mosquito-borne infection control and prevention." Infection, Disease & Health 23, no. 2 (2018): 114-120.
head(sl_dengue_serotype)head(sl_dengue_serotype)
Sri Lanka is divided into 9 provinces, each comprising several districts. Here is a list of the districts and the provinces to which they belong.
Name of the province
Name of the district
sl_province_districtssl_province_districts
An object of class tbl_df (inherits from tbl, data.frame) with 26 rows and 2 columns.
https://moe.gov.lk/ministry-2/provinces/
sl_province_districtssl_province_districts
Total number of premises inspected: 279,728; Total number of premises inspected: 279,728; total Ae. aegypti–positive containers: 9,699. Other miscellaneous items include refrigerator trays, nonfunctional cisterns, pet feeding cups, gutters, concrete slabs, and any other water-collecting containers. (Last accessed from the source on 3 September 2024).
sl_sitessl_sites
A tibble with 9 rows and 7 variables:
Province
Percentage of water-retaining containers positive for discarded items
Percentage of water-retaining containers positive for water storage containers and tanks
Percentage of water-retaining containers positive for ponds and ornamental items
Percentage of water-retaining containers positive for wells and tube wells
Percentage of water-retaining containers positive for natural water collections
Percentage of water-retaining containers positive for other miscellaneous items
Tissera, H.A., Jayamanne, B.D., Raut, R., Janaki, S.M., Tozan, Y., Samaraweera, P.C., Liyanage, P., Ghouse, A., Rodrigo, C., de Silva, A.M. and Fernando, S.D., 2020. Severe dengue epidemic, Sri Lanka, 2017. Emerging infectious diseases, 26(4), p.682. head(sl_sites)
Weekly cases of dengue in Sri Lanka
srilanka_weekly_datasrilanka_weekly_data
A tibble with 23815 rows and 6 variables:
year
week number
starting date of the week
ending date of the week
district name
Number of dengue cases
Weekly Epidemiological Reports, Epidemiology Unit, Ministry of Health, Sri Lanka.
head(srilanka_weekly_data)head(srilanka_weekly_data)
Annual indigenous and imported dengue cases in Taiwan, 1987-2023.
taiwan_denguetaiwan_dengue
A tibble with 37 rows and 3 variables:
Year
Number of indigenous dengue cases
Number of imported dengue
Taiwan Centres for Disease Control, Available at: https://www.cdc.gov.tw/En/Category/ListContent/bg0g_VU_Ysrgkes_KRUDgQ?uaid=9_Oq7OYHa-l8B05iUwyVvQ. (Accessed: 4 September 2024), Source 2: Weekly Dengue Updates, National Dengue Control Unit, Ministry of Health
head(taiwan_dengue)head(taiwan_dengue)
Annual incidence of dengue around the world
world_annualworld_annual
A tibble with 6750 rows and 4 variables:
Longitude
Latitude
group variable
collect in order
regions
subregions
Country or area code
year
Number of dengue incidence across all ages
#'
whetherdengue cases present or not
https://ourworldindata.org/grapher/dengue-incidence
head(world_annual)head(world_annual)